6MXZ

Structure of 53BP1 Tudor domains in complex with small molecule UNC3474

• PDB DOI:  https://doi.org/10.2210/pdb6MXZ/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-31 Released: 2019-11-27 
• Deposition Author(s): Cui, G., Botuyan, M.V., Schuller, D.J., Mer, G.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.223 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Structure of 53BP1 Tudor domains in complex with small molecule UNC3474

Cui, G., Botuyan, M.V., Schuller, D.J., Mer, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 141.15 kDa 
• Atom Count: 11,450 
• Modelled Residue Count: 1,195 
• Deposited Residue Count: 1,230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TP53-binding protein 1	A, B, C, D, E, F, G, H, I, J	123	Homo sapiens	Mutation(s): 0  Gene Names: TP53BP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12888 (Homo sapiens) Explore Q12888  Go to UniProtKB:  Q12888
PHAROS:  Q12888

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K6S	K [auth A], M [auth D], P [auth E], T [auth H], V [auth I]	N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide C17 H28 N2 O CNTJLQUUYDXEFL-UHFFFAOYSA-N
FMT	L [auth B], N [auth D], O [auth D], Q [auth F], R [auth F], S [auth G], U [auth H]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
K6S	BindingDB:  6MXZ	IC50: 1.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.223 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.665	α = 90
b = 160.708	β = 90
c = 182.647	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-27 
Deposition Author(s): Cui, G., Botuyan, M.V., Schuller, D.J., Mer, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA132878

Revision History  

• Version 1.0: 2019-11-27
  Type: Initial release